Hyperlink Management System is a system for automatically updating and maintaining hyperlinks among major public databases in the field of life science. Everyday, we create corresponding tables of data IDs that are used in major databases for genes and proteins, and provide a cgi-program that returns correct and up-to-date URLs of corresponding data in many databases.
By using the CGI program on this server, users can easily create hyperlinks to major databases in their own databases and homepages. Furthermore, on this web site, we provide useful tools such as "All Database Search", "ID converter system", and "Downloading ID tables".
This System was developed at the Biological Information Research Center of the National Institute of Advanced Industrial Science and Technology (AIST) with the financial support from the JST (2006-2008). Since 2008, the system is developed at the Biomedicinal Information Research Center of AIST with a support from the Integrated Database Project of the Ministry of Economy, Trade and Industry of Japan (a portal for the project: MEDALS).
This work is licensed under a Creative Commons Attribution 2.1 Japan License.
Please cite the paper below if you utilize the systems provided on
this web site.
Imanishi T and Nakaoka H (2009) Hyperlink Management System and ID
Converter System: enabling maintenance-free hyperlinks among major
biological databases. Nucleic Acids Research 37(Web Server Issue)
doi:10.1093/nar/gkp355. (http://biodb.jp/)
In order to create hyperlinks using the CGI-program of the Hyperlink Management System, use the following URL as a target URL..
http://biodb.jp/hfs.cgi?id=[ID]&type=[ID Type]&db=[Database Name] |
Sample
The hyperlink to the "Transcript view" of H-InvDB using the INSD accession number "BC053657" will be the following URL.
http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW |
<a href='http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW'>BC053657</a> Sample：BC053657 |
| No. | Format | Outline |
|---|---|---|
| 1 | ACC_ID | Accession Number |
| 2 | HIT_ID | H-Inv transcript ID (HIT) |
| 3 | HIX_ID | H-Inv cluster ID (HIX) |
| 4 | HIP_ID | H-Inv protein ID (HIP) |
| 5 | UNIPROT_ID | UniProt Accession Number |
| 6 | GENE_SYMBOL | HUGO gene symbol |
| 7 | REF_SEQ | RefSeq |
| 8 | OMIM_ID | OMIM ID |
| 9 | GENE_ID | GeneID |
| 10 | PUBMED_ID | PubMed ID |
| 11 | JSNP_ID | dbSNP rs# |
| 12 | MS_ID | Marker Name |
| 13 | PDB_ID | PDB ID |
| 14 | FR_ID | fRNAdb ID |
| 15 | ENST_ID | Ensembl Transcript ID |
| 16 | ENSG_ID | Ensembl Gene ID |
| 17 | CLONE_ID | Clone ID (by NBRC) |
| 18 | FLJ_ID | FLJ ID (by NBRC) |
| 19 | HPRD_ID | HPRD ID |
| 20 | CIPRO_ID | CIPRO ID |
| No. | Format | Outline |
|---|---|---|
| 1 | MMU_MGI_ID | MGI ID |
| 2 | MMU_ACC_ID | Accession Number |
| 3 | HIT_ID | H-Inv transcript ID (HIT) |
| 4 | MMU_UNIPROT_ID | UniProt Accession Number |
| 5 | MMU_REF_SEQ | RefSeq |
| 6 | MMU_GENE_ID | GeneID |
| 7 | MMU_PUBMED_ID | PubMed ID |
| 8 | MMU_ENST_ID | Ensembl Transcript ID |
| 9 | MMU_ENSG_ID | Ensembl Gene ID |
| 10 | MMU_CLONE_ID | Clone ID(FANTOM) |
| No. | Format | Outline |
|---|---|---|
| 1 | TRANSCRIPTVIEW | H-InvDB (Transcript view) |
| 2 | LOCUSVIEW | H-InvDB (Locus view) |
| 3 | GINTEGRA | H-InvDB (G-integra) |
| 4 | PPI | H-InvDB (PPI view) |
| 5 | NUCLEOTIDE | NCBI (Nucleotide) |
| 6 | GENBANK | NCBI (GenBank) |
| 7 | ENTREZGENE | NCBI (Entrez Gene) |
| 8 | OMIM | NCBI (OMIM) |
| 9 | PUBMED | NCBI (PubMed) |
| 10 | GEMDBJ | GeMDBJ |
| 11 | HUGO | HUGO |
| 12 | MUTATIONVIEW | MutationView |
| 13 | HGOLD | H-GOLD |
| 14 | PDB | PDB |
| 15 | UNIPROT | UniProt |
| 16 | ENST | Ensembl Transcriptview |
| 17 | ENSG | Ensembl Geneview |
| 18 | GGDB | GGDB |
| 19 | FRNADB | fRNAdb |
| 20 | NBRC | NBRC |
| 21 | HGPD | HGPD |
| 22 | KEGG | KEGG Gene |
| 23 | PATHWAY | KEGG Pathway |
| 24 | HPRD | HPRD |
| 25 | LEGENDA | LEGENDA |
| 26 | EVOLA | EVOLA |
| 27 | HDBAS | H-DBAS |
| 28 | GCOMPASS | G-Compass |
| 29 | PROTEINVIEW | Protein View |
| 30 | CIPRO | CIPRO |
| 31 | HANGEL | H-ANGEL |
| 32 | FLJH | FLJ Human cDNA |
| 33 | VARYSYSDB | VarySysDB |
| No. | Format | Outline |
|---|---|---|
| 1 | NUCLEOTIDE | NCBI (Nucleotide) |
| 2 | GENBANK | NCBI (GenBank) |
| 3 | ENTREZGENE | NCBI (Entrez Gene) |
| 4 | PUBMED | NCBI (PubMed) |
| 5 | UNIPROT | UniProt |
| 6 | ENST | Ensembl Transcriptview |
| 7 | ENSG | Ensembl Geneview |
| 8 | KEGG | KEGG Gene |
| 9 | PATHWAY | KEGG Pathway |
| 10 | EVOLA | EVOLA |
| 11 | MGI | MGI |
| 12 | IKMC | IKMC |
| 13 | FANTOM | FANTOM |
By a web-service connection to the Real-Time Link Generator of Hyperlink Forwarding System, you can show hyperlinks only when data exists at the destination. This is useful because users can know whether the link is active or not. If there is no data at the destination, "No Link" will be shown.
Please see the HTML sources of the following two examples, and copy and paste them as you like (you need to change only IDs).
Sample 1
Sample 2
The sample 1 shows hyperlinks to Locus view of H-InvDB based on a OMIM ID. The sample 2 shows hyperlinks to 24 kinds of databases. By simply inserting several lines of JavaScript in your HTML, you can use this function.
By specifying IDs of any kind, this system searches for IDs in other databases that correspond to the specified IDs. By default, [All Databases] is selected as a database to open.
You can download corresponding tables of two IDs. Select two IDs, push the search button, and start downloading the file of corresponding tables. The files are in tab-delimited text format.
This system acquires data from the following data bases.
We analyze correspondence of data IDs based on the following ID networks. By tracing the paths connected by solid lines, we make corresponding tables for all possible pairs of IDs.
H-InvDB http://www.h-invitational.jp/hinv/ahg-db/index.jsp
-Accession Number |
NCBI http://www.ncbi.nlm.nih.gov/
-Accession Number |
HUGO http://www.genenames.org/
-HUGO gene symbol |
H-GOLD http://www.h-invitational.jp/gdbs/
-Accession Number |
GeMDBJ https://gemdbj.nibio.go.jp/
-HUGO gene symbol |
PDBj http://www.pdbj.org/
-UniProt Accession Number |
MutationView http://mutview.dmb.med.keio.ac.jp/MutationView/jsp/mutview/index.jsp
-HUGO gene symbol |
Ensembl http://www.ensembl.org/index.html
-HUGO gene symbol |
UniProt http://www.uniprot.org/
-UniProt Accession Number |
fRNAdb http://www.ncrna.org/frnadb
-Accession Number |
GGDB http://riodb.ibase.aist.go.jp/rcmg/ggdb/
-HUGO Gene Symbol |
HGPD http://www.HGPD.jp/
-Accession Number |
KEGG http://www.genome.jp/kegg/
-GeneID |
HPRD http://www.hprd.org/
-GeneID |
NBRC http://www.nbrc.nite.go.jp/e/index.html
-Accession Number |
LEGENA http://h-invitational.jp/legenda/top.htm
-GeneID |
Evola http://www.h-invitational.jp/evola/search.html
-Mouse Accession Number |
H-DBAS http://h-invitational.jp/h-dbas/
-Accession Number |
G-Compass http://h-invitational.jp/g-compass/
-Accession Number |
Protein View http://h-invitational.jp/hinv/help/help_index.html
-Accession Number |
CIPRO http://cipro.ibio.jp/
-Accession Number |
H-ANGEL http://h-invitational.jp/hinv/h-angel/
-Accession Number |
FLJ Human cDNA http://flj.hinv.jp/
-Accession Number |
VarySysDB http://h-invitational.jp/varygene/home.htm
-Accession Number |
NCBI http://www.ncbi.nlm.nih.gov/
-Accession Number |
Ensembl http://www.ensembl.org/index.html
-HUGO gene symbol |
UniProt http://www.uniprot.org/
-UniProt Accession Number |
KEGG http://www.genome.jp/kegg/
-GeneID |
Evola http://www.h-invitational.jp/evola/search.html
-H-Inv transcript ID(HIT) |
MGI http://www.informatics.jax.org/
-MGI ID |
IKMC http://www.knockoutmouse.org
-MGI ID |
FANTOM http://fantom3.gsc.riken.jp/
-Mouse Accession Number |
